If you are summing over the length of the rear wall of the port to compute a nominal port length, then I believe that will give a slight overestimate of the port length. The length of the port might be better approximated by summing the length of the port through the centre of the vertical cross-section. That will be a little bit shorter than the length of the rear wall of the port. There is also an "end correction" that needs to be added to the physical length of the port. What does WinISD suggest will be the end correction? Does it include the end correction in its computations?
It would also be helpful if your drawings included dimensions, ideally in mm, although inches would suffice.
If you'd like to share your WinISD project file, I can take a look at the design of the low-frequency alignment to give me a better idea of what you're trying to achieve. I think you can attach files, if the button below this message is anything to go by.